Snakemake Report

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Workflow

human_genomics_pipeline processes paired-end sequencing data (WGS or WES) using bwa, sambamba and GATK4. It is based on the GATK4 best practices for data pre-processing for variant discovery

Run parameters:

Input data type: Single
Reference genome: /store/lkemp/publicData/referenceGenome/gatkBundle/GRCh37/ucsc.hg19.fasta
dbSNP database /store/lkemp/publicData/dbSNP/gatkBundle/GRCh37/dbsnp_138.hg19.vcf

Click the nodes to obtain details about each step.

Base recalibration

Quality checks

Trimming

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Jobs 1

Input files

qc/fastqc/NIST7035_NIST_R1_fastqc.zip
qc/fastqc/NIST7086_NIST_R1_fastqc.zip
qc/fastqc/NIST7035_NIST_R2_fastqc.zip
qc/fastqc/NIST7086_NIST_R2_fastqc.zip

Output files

qc/multiqc/pre_trim_multiqc_report.html

Conda software stack

bioconda::multiqc =1.8

Code

1	`multiqc {input} -o qc/multiqc/ -i pre_trim`

Jobs 1

Input files

trim_galore/NIST7035_NIST_R1_val_1_fastqc.zip
trim_galore/NIST7086_NIST_R1_val_1_fastqc.zip
trim_galore/NIST7035_NIST_R2_val_2_fastqc.zip
trim_galore/NIST7086_NIST_R2_val_2_fastqc.zip

Output files

qc/multiqc/post_trim_multiqc_report.html

Conda software stack

bioconda::multiqc =1.8

Code

1	`multiqc {input} -o qc/multiqc/ -i post_trim`

Jobs 2

Input files

mapped/{sample}_bwa_recal.bam
/store/lkemp/publicData/referenceGenome/gatkBundle/GRCh37/ucsc.hg19.fasta
/store/lkemp/publicData/dbSNP/gatkBundle/GRCh37/dbsnp_138.hg19.vcf

Output files

vcf/{sample}_raw_snps_indels_AS_g.vcf

Conda software stack

bioconda::gatk4 =4.1.6.0

Code

1	`gatk HaplotypeCaller -I {input.bams} -R {input.refgenome} -D {input.dbsnp} -O {output} --tmp-dir {params.tdir} --native-pair-hmm-threads {threads} {params.padding} {params.intervals}`

Jobs 2

Input files

../fastq/{sample}_R1.fastq.gz
../fastq/{sample}_R2.fastq.gz

Output files

qc/fastqc/{sample}_R1_fastqc.html
qc/fastqc/{sample}_R2_fastqc.html
qc/fastqc/{sample}_R1_fastqc.zip
qc/fastqc/{sample}_R2_fastqc.zip

Conda software stack

bioconda::fastqc =0.11.9

Code

1	`fastqc {input.R1} {input.R2} --outdir qc/fastqc 2> {log} --threads {threads}`

Jobs 2

Input files

../fastq/{sample}_R1.fastq.gz
../fastq/{sample}_R2.fastq.gz

Output files

trim_galore/{sample}_R1_val_1.fq.gz
trim_galore/{sample}_R2_val_2.fq.gz
trim_galore/{sample}_R1_val_1_fastqc.zip
trim_galore/{sample}_R2_val_2_fastqc.zip
trim_galore/{sample}_R1.fastq.gz_trimming_report.txt
trim_galore/{sample}_R2.fastq.gz_trimming_report.txt

Conda software stack

bioconda::trim-galore =0.6.5

Code

1	`trim_galore --paired {input.R1} {input.R2} -o trim_galore/ {params}`

Jobs 2

Input files

mapped/{sample}_sorted_mkdups_rgreplaced.bam
mapped/{sample}_sorted_mkdups_rgreplaced.bam.bai
mapped/{sample}_recalibration_report.grp
/store/lkemp/publicData/referenceGenome/gatkBundle/GRCh37/ucsc.hg19.fasta

Output files

mapped/{sample}_bwa_recal.bam

Conda software stack

bioconda::gatk4 =4.1.6.0

Code

1	`gatk ApplyBQSR -I {input.bams} -bqsr {input.recal} -R {input.refgenome} -O {output} {params.padding} {params.intervals}`

Jobs 2

Input files

mapped/{sample}_bwamem_sorted_mkdups.bam

Output files

mapped/{sample}_sorted_mkdups_rgreplaced.bam

Conda software stack

bioconda::gatk4 =4.1.6.0

Code

1	`gatk AddOrReplaceReadGroups -I {input} -O {output} --TMP_DIR {params.tdir} {params.other}`

Jobs 2

Input files

mapped/{sample}_sorted_mkdups_rgreplaced.bam

Output files

mapped/{sample}_sorted_mkdups_rgreplaced.bam.bai

Conda software stack

bioconda::sambamba =0.7.0

Code

1	`sambamba index -p {input} -t {threads}`

Jobs 2

Input files

mapped/{sample}_sorted_mkdups_rgreplaced.bam
mapped/{sample}_sorted_mkdups_rgreplaced.bam.bai
/store/lkemp/publicData/referenceGenome/gatkBundle/GRCh37/ucsc.hg19.fasta
/store/lkemp/publicData/dbSNP/gatkBundle/GRCh37/dbsnp_138.hg19.vcf
/store/lkemp/publicData/dbSNP/gatkBundle/GRCh37/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz
/store/lkemp/publicData/dbSNP/gatkBundle/GRCh37/1000G_phase1.indels.hg19.sites.vcf.gz

Output files

mapped/{sample}_recalibration_report.grp

Conda software stack

bioconda::gatk4 =4.1.6.0

Code

1	`gatk BaseRecalibrator -I {input.bams} -R {input.refgenome} --known-sites {input.dbsnp} --known-sites {input.mills} --known-sites {input.indels} -O {output} {params.padding} {params.intervals}`

Jobs 2

Input files

mapped/{sample}_bwamem_sorted.bam

Output files

mapped/{sample}_bwamem_sorted_mkdups.bam
mapped/{sample}_bwamem_sorted_mkdups.bam.bai

Conda software stack

bioconda::sambamba =0.7.0

Code

1	`sambamba markdup -p {input} {output.bam} --tmpdir={params.tdir} {params.other} -t {threads}`

Jobs 2

Input files

mapped/{sample}_bwamem.bam

Output files

mapped/{sample}_bwamem_sorted.bam
mapped/{sample}_bwamem_sorted.bam.bai

Conda software stack

bioconda::sambamba =0.7.0

Code

1	`sambamba sort -p {input} -o {output.bams} --tmpdir={params.tdir} {params.other} -t {threads}`

Jobs 2

Input files

/store/lkemp/publicData/referenceGenome/gatkBundle/GRCh37/ucsc.hg19.fasta
trim_galore/{sample}_R1_val_1.fq.gz
trim_galore/{sample}_R2_val_2.fq.gz

Output files

mapped/{sample}_bwamem.bam

Conda software stack

bioconda::samtools =1.10
bioconda::bwa =0.7.17

Code

1	`bwa mem {input.refgenome} {input.R1} {input.R2} -t {threads} -M \| samtools view -@ {threads} -Sbh - > {output}`